I have two questions regarding ballgown:

1) Why is ballgown using FPKM for the stat. test and not counts? Is there an advantage or is this historical?

2) I guess ballgown does test transcripts "on an individual level" for differential expression, right? What I mean is: if one gene has two isoforms, it will not "understand" if for a condition suddenly one isoform gets expressed instead of the other? As far as I understand it will test them individually? --> So if I am right, then if two transcripts (roughly same length) belong to the same gene and in the first condition only isoform 1 is expressed with , let's say 1000 fragments and in second condition only isoform 2 is expressed also with 1000 fragments, then there will probably be no stat. significant result for this gene, although the change is dramatic....? But on the transcript level this would probably be significant, without the test "understanding" that the two changes are probably linked?